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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ), 'gf_id' => 'HOM05D001258', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001258' ), 'data_identifier' => 'HOM05D001258', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001258', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '497', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p37310' => 'bna', 'A03p17980' => 'bna', 'A03p40030' => 'bna', 'A03p46180' => 'bna', 'A04p05790' => 'bna', 'A05p32710' => 'bna', 'A05p43930' => 'bna', 'A06p31180' => 'bna', 'A07p21890' => 'bna', 'A09p45600' => 'bna', 'A09p46910' => 'bna', 'Aa31LG10G8870' => 'aar', 'Aa31LG5G13730' => 'aar', 'Aa31LG8G4050' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3133' => 'aag', 'Actinidia01594' => 'ach', 'Actinidia12998' => 'ach', 'Actinidia13815' => 'ach', 'Actinidia15606' => 'ach', 'Actinidia17175' => 'ach', 'Actinidia18453' => 'ach', 'Actinidia26546' => 'ach', 'Actinidia28179' => 'ach', 'Actinidia29162' => 'ach', 'Actinidia40375' => 'ach', 'Ah.04g157170' => 'amhyb', 'Ah.04g157180' => 'amhyb', 'Ah.08g220310' => 'amhyb', 'AL3G12870' => 'aly', 'AL3G30000' => 'aly', 'AL5G34990' => 'aly', 'Aqoxy1G00789' => 'aox', 'Aqoxy2G02737' => 'aox', 'Aqoxy3G04143' => 'aox', 'Aqoxy3G04144' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0CM1H8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.0SFT85' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31U4BG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.56WBIF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5U4ZXD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5Y48JI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.A0NCLF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.SHPI4E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U735UZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UNS5A9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VQB8P7' => 'arhy', 'AT3G03270' => 'ath', 'AT3G17020' => 'ath', 'AT3G53990' => 'ath', 'ATR0210G006' => 'atr', 'ATR0598G014' => 'atr', 'ATR0796G070' => 'atr', 'ATR1152G099' => 'atr', 'Atru.chr1.1972' => 'acertr', 'Atru.chr8.2105' => 'acertr', 'AUR62001721' => 'cqu', 'AUR62016195' => 'cqu', 'AUR62016196' => 'cqu', 'AUR62020060' => 'cqu', 'AUR62039292' => 'cqu', 'BcaB01g00226' => 'bca', 'BcaB02g07757' => 'bca', 'BcaB02g08496' => 'bca', 'BcaB03g14932' => 'bca', 'BcaB04g18511' => 'bca', 'BcaB04g18923' => 'bca', 'BcaB06g25794' => 'bca', 'BcaB08g34567' => 'bca', 'BcaC01g03794' => 'bca', 'BcaC02g09116' => 'bca', 'BcaC02g10067' => 'bca', 'BcaC05g28836' => 'bca', 'BcaC05g29874' => 'bca', 'BcaC05g30310' => 'bca', 'BcaC07g39747' => 'bca', 'BcaC08g44657' => 'bca', 'BcaC09g48653' => 'bca', 'BolC1t04695H' => 'bol', 'BolC3t17134H' => 'bol', 'BolC4t25437H' => 'bol', 'BolC5t33687H' => 'bol', 'BolC5t35022H' => 'bol', 'BolC6t37366H' => 'bol', 'BolC8t50521H' => 'bol', 'BraA01t03789Z' => 'bra', 'BraA03t13151Z' => 'bra', 'BraA04t16276Z' => 'bra', 'BraA05t22093Z' => 'bra', 'BraA05t23129Z' => 'bra', 'BraA07t29870Z' => 'bra', 'BraA09t40021Z' => 'bra', 'BraA09t40158Z' => 'bra', 'C01p47250' => 'bna', 'C03p48560' => 'bna', 'C04p38600' => 'bna', 'C05p49410' => 'bna', 'C05p63550' => 'bna', 'C06p21770' => 'bna', 'C08p29200' => 'bna', 'CAN.G230.7' => 'can', 'CAN.G244.6' => 'can', 'CAN.G334.3' => 'can', 'CAN.G334.4' => 'can', 'CAN.G334.5' => 'can', 'CAN.G525.2' => 'can', 'CANSAT35G0723' => 'cansat', 'CANSAT78G0687' => 'cansat', 'CANSAT78G2077' => 'cansat', 'CARHR077290' => 'chi', 'CARHR092270' => 'chi', 'CARHR163890' => 'chi', 'Carub.0003s0242' => 'cru', 'Carub.0003s1677' => 'cru', 'Carub.0005s2058' => 'cru', 'Ca_05770_v3' => 'car', 'Ca_07579_v3' => 'car', 'Ca_20608_v3' => 'car', 'Ca_25873_v3' => 'car', 'Ca_28000_v3' => 'car', 'Ca_29562_v3' => 'car', 'Ca_30564_v3' => 'car', 'CBR_g23470' => 'cbr', 'Cc03_g00910' => 'ccan', 'Cc06_g02020' => 'ccan', 'Cc07_g12920' => 'ccan', 'CDE02G0191' => 'cde', 'CDE02G4708' => 'cde', 'CDE03G0257' => 'cde', 'CDE04G2065' => 'cde', 'CDE04G2658' => 'cde', 'Cfa007766' => 'cfa', 'Cfa011589' => 'cfa', 'Cfa015323' => 'cfa', 'Cfa017295' => 'cfa', 'Ciclev10002725m.g' => 'ccl', 'Ciclev10006081m.g' => 'ccl', 'Ciclev10012955m.g' => 'ccl', 'Ciclev10029414m.g' => 'ccl', 'CiPaw.01G139000' => 'cil', 'CiPaw.02G075400' => 'cil', 'CiPaw.02G196800' => 'cil', 'CiPaw.03G077100' => 'cil', 'CiPaw.09G202500' => 'cil', 'CiPaw.09G202600' => 'cil', 'CiPaw.10G150000' => 'cil', 'CiPaw.11G143300' => 'cil', 'CiPaw.13G087000' => 'cil', 'CiPaw.14G027500' => 'cil', 'CiPaw.14G063700' => 'cil', 'CiPaw.16G063900' => 'cil', 'ClCG01G008640' => 'cla', 'ClCG05G006520' => 'cla', 'ClCG10G021580' => 'cla', 'COL.COLO4_14690' => 'col', 'COL.COLO4_19052' => 'col', 'COL.COLO4_34629' => 'col', 'Cpa.g.sc56.65' => 'cpa', 'Cpa.g.sc9.67' => 'cpa', 'CsaV3_3G015130' => 'csa', 'CsaV3_3G034440' => 'csa', 'CSS0001841' => 'camsi', 'CSS0012118' => 'camsi', 'CSS0016006' => 'camsi', 'CSS0018834' => 'camsi', 'CSS0018862' => 'camsi', 'CSS0021972' => 'camsi', 'CSS0035283' => 'camsi', 'CSS0044474' => 'camsi', 'CSS0044909' => 'camsi', 'CSS0045188' => 'camsi', 'DCAR_003412' => 'dca', 'DCAR_023353' => 'dca', 'DCAR_026999' => 'dca', 'Dinv05616' => 'din', 'Dinv08627' => 'din', 'Dinv15185' => 'din', 'Dinv28232' => 'din', 'Dinv34305' => 'din', 'Dinv35539' => 'din', 'Dinv37109' => 'din', 'Duzib052G0406' => 'dzi', 'Duzib093G2015' => 'dzi', 'Duzib106G0623' => 'dzi', 'Duzib106G0639' => 'dzi', 'Duzib106G1662' => 'dzi', 'Duzib151G0296' => 'dzi', 'Duzib168G0926' => 'dzi', 'Duzib170G0306' => 'dzi', 'ECA238G0440' => 'eca', 'ECA246G0721' => 'eca', 'ECA246G0779' => 'eca', 'ECA246G2618' => 'eca', 'ECA247G0463' => 'eca', 'EL10Ac3g05488' => 'bvu', 'EL10Ac3g05490' => 'bvu', 'EL10Ac7g16091' => 'bvu', 'Eucgr.A00373' => 'egr', 'Eucgr.B02294' => 'egr', 'Eucgr.B02732' => 'egr', 'Eucgr.F02899' => 'egr', 'FAN05G3906' => 'fan', 'FAN07G2205' => 'fan', 'FAN09G1443' => 'fan', 'FAN11G1978' => 'fan', 'FAN12G0951' => 'fan', 'FAN14G0845' => 'fan', 'FAN16G2034' => 'fan', 'FAN21G3486' => 'fan', 'FAN23G1012' => 'fan', 'FAN25G1240' => 'fan', 'FvH4_3g37220' => 'fve', 'FvH4_4g19580' => 'fve', 'FvH4_6g12670' => 'fve', 'Glyma.01G106200' => 'gma', 'Glyma.02G241601' => 'gma', 'Glyma.03G073710' => 'gma', 'Glyma.07G140800' => 'gma', 'Glyma.09G036100' => 'gma', 'Glyma.11G134900' => 'gma', 'Glyma.12G058500' => 'gma', 'Glyma.14G211300' => 'gma', 'Glyma.15G141000' => 'gma', 'Glyma.18G190700' => 'gma', 'Gohir.A02G054002' => 'ghi', 'Gohir.A03G046500' => 'ghi', 'Gohir.A03G046600' => 'ghi', 'Gohir.A04G086000' => 'ghi', 'Gohir.A09G066000' => 'ghi', 'Gohir.A09G066100' => 'ghi', 'Gohir.A13G078600' => 'ghi', 'Gohir.D02G058850' => 'ghi', 'Gohir.D03G120600' => 'ghi', 'Gohir.D03G120700' => 'ghi', 'Gohir.D04G125700' => 'ghi', 'Gohir.D09G065200' => 'ghi', 'Gohir.D09G065300' => 'ghi', 'Gohir.D13G095700' => 'ghi', 'Gorai.001G247900' => 'gra', 'Gorai.003G127300' => 'gra', 'Gorai.003G127400' => 'gra', 'Gorai.005G066600' => 'gra', 'Gorai.006G079900' => 'gra', 'Gorai.006G080000' => 'gra', 'Gorai.012G108900' => 'gra', 'GSVIVG01024846001' => 'vvi', 'GSVIVG01034055001' => 'vvi', 'GSVIVG01035004001' => 'vvi', 'GSVIVG01035248001' => 'vvi', 'HanXRQChr01g0012901' => 'han', 'HanXRQChr04g0125641' => 'han', 'HanXRQChr05g0148271' => 'han', 'HanXRQChr10g0291901' => 'han', 'HanXRQChr16g0532241' => 'han', 'HanXRQChr17g0547091' => 'han', 'HanXRQChr17g0554941' => 'han', 'Haze_01292' => 'cav', 'Haze_14307' => 'cav', 'Haze_20898' => 'cav', 'Haze_24207' => 'cav', 'Hma1.2p1_0013F.1_g008640' => 'hma', 'Hma1.2p1_0671F.1_g200640' => 'hma', 'Hma1.2p1_1521F.1_g288660' => 'hma', 'HPP92_017246' => 'vpl', 'HPP92_019336' => 'vpl', 'HPP92_019859' => 'vpl', 'HPP92_027564' => 'vpl', 'Hund03120' => 'sun', 'Hund11966' => 'sun', 'Hund11968' => 'sun', 'Lalb_Chr01g0022801' => 'lal', 'Lalb_Chr03g0026361' => 'lal', 'Lalb_Chr03g0042751' => 'lal', 'Lalb_Chr10g0104111' => 'lal', 'Lalb_Chr15g0089201' => 'lal', 'Lalb_Chr19g0124981' => 'lal', 'Lj1g0001551' => 'lja', 'Lj2A513T57' => 'lonja', 'Lj2C85T6' => 'lonja', 'Lj3C960T3' => 'lonja', 'Lj3g0016520' => 'lja', 'Lj3g0021934' => 'lja', 'Lj6A690T72' => 'lonja', 'Lj6g0009519' => 'lja', 'LjContig00141g0005731' => 'lja', 'LjContig00141g0006229' => 'lja', 'Lsat_1_v5_gn_3_67180' => 'lsa', 'Lsat_1_v5_gn_6_116261' => 'lsa', 'Lsat_1_v5_gn_8_84020' => 'lsa', 'Lsat_1_v5_gn_9_30421' => 'lsa', 'Manes.02G080300' => 'mes', 'Manes.03G204201' => 'mes', 'Manes.08G082400' => 'mes', 'Manes.09G098760' => 'mes', 'Manes.15G005000' => 'mes', 'Mapoly0031s0130' => 'mpo', 'Mapoly0094s0001' => 'mpo', 'Mapoly0130s0028' => 'mpo', 'Mapoly0510s0002' => 'mpo', 'MBI05_g02673_MAGBIO' => 'mbi', 'MBI13_g30067_MAGBIO' => 'mbi', 'MBI13_g40631_MAGBIO' => 'mbi', 'MBI13_g44545_MAGBIO' => 'mbi', 'MBI14_g02859_MAGBIO' => 'mbi', 'MBI16_g14598_MAGBIO' => 'mbi', 'MBI17_g20943_MAGBIO' => 'mbi', 'MBI18_g17307_MAGBIO' => 'mbi', 'MBI19_g02941_MAGBIO' => 'mbi', 'MBI19_g03228_MAGBIO' => 'mbi', 'MCO04G398' => 'mco', 'MD03G1082800' => 'mdo', 'MD04G1139800' => 'mdo', 'MD09G1276200' => 'mdo', 'MD12G1155300' => 'mdo', 'MD13G1155500' => 'mdo', 'MD16G1155000' => 'mdo', 'MD17G1270300' => 'mdo', 'Medtr2g034200' => 'mtr', 'Medtr4g019800' => 'mtr', 'Medtr4g064933' => 'mtr', 'Medtr5g077130' => 'mtr', 'Medtr6g038080' => 'mtr', 'Medtr7g065770' => 'mtr', 'MELO3C006711.2' => 'cme', 'MELO3C009215.2' => 'cme', 'MELO3C025079.2' => 'cme', 'Migut.G00052' => 'egut', 'Migut.J00261' => 'egut', 'Migut.K01096' => 'egut', 'Migut.K01097' => 'egut', 'Migut.K01104' => 'egut', 'MSTRG.26786' => 'ama', 'MSTRG.3681' => 'ama', 'MSTRG.3860' => 'ama', 'Nitab4.5_0000008g0210' => 'nta', 'Nitab4.5_0000119g0390' => 'nta', 'Nitab4.5_0000169g0200' => 'nta', 'Nitab4.5_0000574g0200' => 'nta', 'Nitab4.5_0002214g0060' => 'nta', 'Nitab4.5_0002218g0050' => 'nta', 'Nitab4.5_0005193g0020' => 'nta', 'Nitab4.5_0005572g0010' => 'nta', 'Nitab4.5_0005572g0020' => 'nta', 'Nitab4.5_0006075g0010' => 'nta', 'Nitab4.5_0008919g0010' => 'nta', 'Nn2g11295' => 'nnu', 'Nn2g13532' => 'nnu', 'Nn3g21714' => 'nnu', 'Nn4g24643' => 'nnu', 'Nn4g25583' => 'nnu', 'Oeu001832.1' => 'oeu', 'Oeu016487.1' => 'oeu', 'Oeu021132.1' => 'oeu', 'Oeu022943.1' => 'oeu', 'Oeu051062.1' => 'oeu', 'Os01g0170600' => 'osa', 'Os01g0849600' => 'osa', 'Os02g0773200' => 'osa', 'Os05g0157200' => 'osa', 'Os05g0170200' => 'osa', 'Os05g0453700' => 'osa', 'Peaxi162Scf00014g00158' => 'pax', 'Peaxi162Scf00132g00910' => 'pax', 'Peaxi162Scf00228g00225' => 'pax', 'Peaxi162Scf00442g00620' => 'pax', 'PGR004G0401' => 'pgr', 'PGR031G0871' => 'pgr', 'PGR031G1435' => 'pgr', 'PGR102G0970' => 'pgr', 'PGSC0003DMG400011721' => 'stu', 'PGSC0003DMG400011722' => 'stu', 'PGSC0003DMG400019138' => 'stu', 'PGSC0003DMG400021844' => 'stu', 'PGSC0003DMG400023615' => 'stu', 'Phvul.006G117600' => 'pvu', 'Phvul.008G113500' => 'pvu', 'Phvul.008G239500' => 'pvu', 'Phvul.010G008900' => 'pvu', 'Phvul.011G060700' => 'pvu', 'Potri.004G075375' => 'ptr', 'Potri.006G092700' => 'ptr', 'Potri.010G144100' => 'ptr', 'Potri.016G104600' => 'ptr', 'Potri.017G144301' => 'ptr', 'Pp3c13_1520' => 'ppa', 'Pp3c20_18710' => 'ppa', 'Pp3c23_2860' => 'ppa', 'Pp3c3_1770' => 'ppa', 'Pp3c8_12890' => 'ppa', 'PRCOL_00001149' => 'pco', 'Prupe.1G118700' => 'ppe', 'Prupe.3G016200' => 'ppe', 'Prupe.6G067100' => 'ppe', 'Prupe.6G265100' => 'ppe', 'Prupe.6G265200' => 'ppe', 'Psat1g160640' => 'psa', 'Psat2g044840' => 'psa', 'Psat2g045560' => 'psa', 'Psat3g134480' => 'psa', 'Psat7g211320' => 'psa', 'Psat7g240560' => 'psa', 'PSO210G1051' => 'pso', 'PSO339G3275' => 'pso', 'PSO384G1595' => 'pso', 'PSO761G0086' => 'pso', 'QL01p028267' => 'qlo', 'QL02p060168' => 'qlo', 'QL02p060239' => 'qlo', 'QL06p011859' => 'qlo', 'QL07p028031' => 'qlo', 'RcHm_v2.0_Chr3g0464511' => 'rch', 'RcHm_v2.0_Chr3g0490231' => 'rch', 'RcHm_v2.0_Chr4g0424841' => 'rch', 'RcHm_v2.0_Chr5g0066971' => 'rch', 'Rhsim02G0004400' => 'rsi', 'Rhsim05G0200500' => 'rsi', 'Rhsim10G0183600' => 'rsi', 'Rhsim13G0076000' => 'rsi', 'Sabra04G0050000' => 'sbr', 'Sabra06G0070400' => 'sbr', 'Sabra10G0111200' => 'sbr', 'Sabra16G0103900' => 'sbr', 'Sabra17G0120500' => 'sbr', 'SalBow4G1901' => 'sbo', 'SalBow5G4902' => 'sbo', 'SalBow5G5217' => 'sbo', 'SalBow5G5723' => 'sbo', 'SalBow8G2198' => 'sbo', 'Sc01g0004890' => 'sci', 'Sc19g0003180' => 'sci', 'Sed0000649' => 'sed', 'Sed0009654' => 'sed', 'Sed0019893' => 'sed', 'SEGI_23258' => 'sgi', 'SEGI_36537' => 'sgi', 'SEGI_39011' => 'sgi', 'SEGI_39310' => 'sgi', 'SGA_v2.0_scaffold104G30092' => 'sas', 'SGA_v2.0_scaffold453G51861' => 'sas', 'SGA_v2.0_scaffold45G17129' => 'sas', 'SMO137G0177' => 'smo', 'SMO144G0075' => 'smo', 'Solyc01g059930.3' => 'sly', 'Solyc04g014600.3' => 'sly', 'Solyc09g011660.3' => 'sly', 'Solyc09g011670.4' => 'sly', 'Solyc10g086670.2' => 'sly', 'Sopen01g026070' => 'spe', 'Sopen04g006740' => 'spe', 'Sopen09g006470' => 'spe', 'Sopen09g006490' => 'spe', 'Sopen10g036080' => 'spe', 'Sp3g02300' => 'spa', 'Sp3g15240' => 'spa', 'Sp5g08410' => 'spa', 'TAR633G0127' => 'tar', 'TAR633G1449' => 'tar', 'TAR636G2115' => 'tar', 'THA.LOC104806539' => 'tha', 'THA.LOC104820302' => 'tha', 'THA.LOC104823399' => 'tha', 'THA.LOC104827230' => 'tha', 'Thecc.04G299400' => 'tca', 'Thecc.05G028000' => 'tca', 'Thecc.09G311700' => 'tca', 'Thhalv10010778m.g' => 'esa', 'Thhalv10021673m.g' => 'esa', 'Thhalv10021680m.g' => 'esa', 'TPR.G10932' => 'tpr', 'TPR.G18879' => 'tpr', 'TPR.G23611' => 'tpr', 'TPR.G27260' => 'tpr', 'TPR.G32562' => 'tpr', 'TWI09G0515' => 'twi', 'TWI53G0298' => 'twi', 'TWI53G0586' => 'twi', 'TWI74G0202' => 'twi', 'TWI77G0198' => 'twi', 'unitig_32.g10633' => 'ugi', 'unitig_32.g11852' => 'ugi', 'unitig_578.g15884' => 'ugi', 'vmacro03018' => 'vma', 'vmacro08056' => 'vma', 'vmacro15185' => 'vma', 'vmacro20200' => 'vma', 'vmacro20484' => 'vma', 'VMungo0331G1206' => 'vmu', 'VMungo0540G0962' => 'vmu', 'VMungo0647G0296' => 'vmu', 'VMungo1127G0273' => 'vmu', 'VMungo1383G0189' => 'vmu', 'Zm00001eb256460' => 'zma', 'Zm00001eb282590' => 'zma', 'Zm00001eb289460' => 'zma', 'Zm00001eb336690' => 'zma', 'Zm00001eb356370' => 'zma', 'Zm00001eb367690' => 'zma' ) $gf_id = 'HOM05D001258' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001258' ) $data_identifier = 'HOM05D001258' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 10, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 5, 'bca' => (int) 17, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 12, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 7, 'dzi' => (int) 8, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 10, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 4, 'han' => (int) 7, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 4, 'sun' => (int) 3, 'lal' => (int) 6, 'lja' => (int) 6, 'lonja' => (int) 4, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 4, 'mbi' => (int) 10, 'mco' => (int) 1, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 4, 'pgr' => (int) 4, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 5, 'ppa' => (int) 5, 'pco' => (int) 1, 'ppe' => (int) 5, 'psa' => (int) 6, 'pso' => (int) 4, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 5, 'sbo' => (int) 5, 'sci' => (int) 2, 'sed' => (int) 3, 'sgi' => (int) 4, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 3, 'tpr' => (int) 5, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 5, 'vmu' => (int) 5, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb367690' $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